modified sequence to accept externally defined loci; modified Individual to have a dob property
Created a simple simulation using Warped object structure.
updated README with info about Warped
changed the genome factory structure. not fully satisfied with the design though. genome factory are no longer singletons which is good (allowing for multiple species with same number of chromosomes, but differing structure). As a result, individuals (species) expect a genome factory as a parameter when creating the individual. Might be just as useful for the Genome Factory to be a friend of an Individual, and produce Individuals. There is a logical error in the design. Individuals don't retain chromosome ids, they simply rely upon an index relative to the genome factory from which they are created. In other words, the index of the chromosome is assumed to be constant across all individuals of the same genome. Thus functions which require chromosome specific information can just jump to the correct chromosome, rather than search for it by id. Conversely, the genome factory organizes chromosomes by id, not index (ie. index changes as chromosomes are added)
Updated Individuals to be only creatable by a GenomeFactory; Considering whether to add a an IndividualFactory
starting to create the basic clotho simulation framework
Merge branch 'revision_0'